1. Biochemistry Lecture 5

2. Protein Functions + PL P L Binding Catalysis Structure

3. Specificity: Lock-and-Key Model Proteins typically have high specificity: only certain ligands bind High specificity can be explained by the complementary of the binding site and the ligand. Complementarity in –size, –shape, –charge, –or hydrophobic / hydrophilic character Lock and Key model by Emil Fisher (1894) assumes that complementary surfaces are preformed. +

4. Specificity: Induced Fit Conformational changes may occur upon ligand binding (Daniel Koshland in 1958). –This adaptation is called the induced fit. –Induced fit allows for tighter binding of the ligand –Induced fit can increase the affinity of the protein for a second ligand Both the ligand and the protein can change their conformations +

5. Oxygen Binding Proteins

6. Binding: Quantitative Description Consider a process in which a ligand (L) binds reversibly to a site in the protein (P) The kinetics of such a process is described by: the association rate constant k a the dissociation rate constant k d After some time, the process will reach the equilibrium where the association and dissociation rates are equal The equilibrium composition is characterized by the the equilibrium constant K a + kaka kbkb PL P L

7. Binding: Analysis in Terms of the Bound Fraction In practice, we can often determine the fraction of occupied binding sites Substituting [PL] with K a [L][P], well eliminate [PL] Eliminating [P] and rearranging gives the result in terms of equilibrium association constant: In terms of the more commonly used equilibrium dissociation constant:

10. Oxygen Binding Proteins

14. Red Blood Cells (erythrocytes)

21. Two Types of the Immune Systems Cellular immune system -targets own cells that have been infected -also clears up virus particles and infecting bacteria -key players: Macrophages, killer T cells (T c ), and inflammatory T cells (TH 1 ) Humoral fluid immune system -targets extracellular pathogens -can also recognize foreign proteins -makes soluble antibodies -keeps memory of past infections -key players: B-lymphocytes and helper T-cells (TH 2 )

34. Myosin In Motion! http://www.youtube.com/watch?v=edBRWl1vftc&feature=player_embedded http://highered.mcgraw- hill.com/sites/0072495855/student_view0/chapter10/animation__myofilament _contraction.html